Modern multidisciplinary sytems (systems of systems, e.g. future energy grids) are too complex to be modelled by a small number of people. Instead, component models developed in different institutes may be coupled in a modular manner (co-simulation). Due to imperfect knowledge of these component models, they have to be treated as black boxes. We present a modular, non-intrusive, ensemble-based uncertainty quantification framework for Smart Grid co-simulation systems considering epistemic as well as aleatory uncertainty.